MICROCIDE PHARMACEUTICALS INC
10-Q, 2000-11-14
PHARMACEUTICAL PREPARATIONS
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                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION

                             Washington, D.C. 20549


                                    FORM 10-Q

(X)  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2000

                                       OR

( )  TRANSITION  REPORT  PURSUANT  TO  SECTION  13 OR  15(d)  OF THE  SECURITIES
     EXCHANGE ACT OF 1934


                         Commission file number: 0-28006


                         MICROCIDE PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)


            Delaware                                           94-3186021
(State or other jurisdiction of                             (I.R.S. Employer
 incorporation of organization)                           Identification Number)


850 Maude Avenue, Mountain View, California                      94043
 (Address of principal executive offices)                      (ZIP Code)

Registrant's telephone number, including area code:           650-428-1550


Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the  preceding 12 months (or for such  shorter  period that the  registrant  was
required  to file  such  reports),  and  (2) has  been  subject  to such  filing
requirements for the past 90 days.

                                   Yes _X_ No ___

Number of shares of Common Stock,  no par value,  outstanding  as of October 31,
2000: 11,409,322


<PAGE>


                         MICROCIDE PHARMACEUTICALS, INC.

                               INDEX FOR FORM 10-Q

                               SEPTEMBER 30, 2000


                                                                           PAGE
                                                                          NUMBER


PART I  FINANCIAL INFORMATION

Item 1. Condensed Financial Statements and Notes (unaudited)

        Condensed Balance Sheets as of September 30, 2000
        and December 31, 1999                                              3

        Condensed Statements of Operations for the three and nine
        months ended September 30, 2000 and September 30, 1999             4

        Condensed Statements of Cash Flows for the nine months
        ended September 30, 2000 and September 30, 1999                    5

        Notes to Condensed Financial Statements                            6

Item 2. Management's Discussion and Analysis of Financial
        Condition and Results of Operations                                8

Item 3. Quantitative and Qualitative Disclosures about Market Risk        12


PART II OTHER INFORMATION                                                 13

Item 1. Legal Proceedings

Item 2. Changes in Securities

Item 3. Defaults in Senior Securities

Item 4. Submission of Matters to a Vote of Security Holders

Item 5. Other Information

Item 6. Exhibits and Reports on Form 8-K


SIGNATURES                                                                14

                                       2

<PAGE>


<TABLE>
                                                   MICROCIDE PHARMACEUTICALS, INC.

                                                      CONDENSED BALANCE SHEETS
                                                           (in thousands)

<CAPTION>
                                                                                                  September 30,         December 31,
                                                                                                      2000                 1999
                                                                                                    --------             --------
                                                                                                  (Unaudited)             (Note)
<S>                                                                                                 <C>                  <C>
ASSETS

Current assets:
  Cash and cash equivalents                                                                         $  2,785             $  5,660
  Short-term investments                                                                              12,439               19,208
  Receivables, prepaid expenses and other current assets                                               1,084                  443
                                                                                                    --------             --------
Total current assets                                                                                  16,308               25,311

Property and equipment, net                                                                            6,239                7,592

Other assets                                                                                             857                  928
                                                                                                    --------             --------

Total assets                                                                                        $ 23,404             $ 33,831
                                                                                                    ========             ========


LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
  Accounts payable                                                                                  $    519             $    358
  Accrued compensation                                                                                 1,053                  984
  Current portion of notes payable                                                                     1,559                1,440
  Deferred revenue                                                                                      --                    387
  Other accrued liabilities                                                                              779                  695
                                                                                                    --------             --------
Total current liabilities                                                                              3,910                3,864

Long-term portion of notes payable                                                                       723                1,907
Accrued rent                                                                                             263                  257

Stockholders' equity:
  Common stock                                                                                        68,296               67,112
  Accumulated deficit                                                                                (49,777)             (39,243)
  Accumulated other comprehensive loss                                                                   (11)                 (66)
                                                                                                    --------             --------

Total stockholders' equity                                                                            18,508               27,803
                                                                                                    --------             --------

Total liabilities and stockholders' equity                                                          $ 23,404             $ 33,831
                                                                                                    ========             ========

NOTE:  The balance  sheet at December  31, 1999 has been  derived from the audited  financial  statements  at that date but does not
include all of the information and footnotes required by generally accepted accounting principles for complete financial statements.

                                            See Notes to Condensed Financial Statements.
</TABLE>

                                                                 3

<PAGE>


<TABLE>
                                                   MICROCIDE PHARMACEUTICALS, INC.

                                                 CONDENSED STATEMENTS OF OPERATIONS
                                              (in thousands, except per share amounts)
                                                             (unaudited)

<CAPTION>
                                                                        Three Months Ended                   Nine Months Ended
                                                                           September 30,                       September 30,
                                                                     --------------------------          --------------------------
                                                                       2000              1999              2000              1999
                                                                     --------          --------          --------          --------
<S>                                                                  <C>               <C>               <C>               <C>
Revenues:
  Research revenues                                                  $  1,454          $  1,560          $  4,108          $  5,498
  Other revenues                                                         --                  32              --                 331
                                                                     --------          --------          --------          --------
       Total revenues                                                   1,454             1,592             4,108             5,829

Operating expenses:
  Research and development                                              3,985             4,044            12,154            13,249
  General and administrative                                            1,242             1,103             3,167             3,087
                                                                     --------          --------          --------          --------
       Total operating expenses                                         5,227             5,147            15,321            16,336
                                                                     --------          --------          --------          --------

Loss from operations                                                   (3,773)           (3,555)          (11,213)          (10,507)

Interest and other income, net                                            210               261               679               848
                                                                     --------          --------          --------          --------
       Net loss                                                      $ (3,563)         $ (3,294)         $(10,534)         $ (9,659)
                                                                     ========          ========          ========          ========


Basic and diluted net loss per share                                 $  (0.31)         $  (0.30)         $  (0.93)         $  (0.87)
                                                                     ========          ========          ========          ========

Weighted-average shares used in computing
   basic and diluted net loss per share                                11,354            11,105            11,292            11,069


                                            See Notes to Condensed Financial Statements.
</TABLE>


                                                                 4

<PAGE>


<TABLE>
                                                   MICROCIDE PHARMACEUTICALS, INC.

                                                 CONDENSED STATEMENTS OF CASH FLOWS
                                                           (in thousands)
                                                             (unaudited)
                                                 Change in cash and cash equivalents

<CAPTION>
                                                                                                         Nine Months Ended
                                                                                                            September 30,
                                                                                                    -------------------------------
                                                                                                      2000                   1999
                                                                                                    --------               --------
<S>                                                                                                 <C>                    <C>
Cash flows used in operating activities:
Net loss                                                                                            $(10,534)              $ (9,659)
Adjustments to reconcile net loss to net cash
   provided by (used in) operating activities:
Depreciation and amortization                                                                          1,926                  2,075
Amortization of deferred compensation                                                                   --                      377
Accrued rent                                                                                               6                    103
Changes in assets and liabilities:
   Receivables, prepaid expenses and other current assets                                               (641)                (1,135)
   Other assets                                                                                           71                     41
   Accounts payable                                                                                      161                   (397)
   Accrued compensation and other accrued liabilities                                                    153                    296
   Deferred revenue                                                                                     (387)                    26
                                                                                                    --------               --------

Net cash used in operating activities                                                                 (9,245)                (8,273)
                                                                                                    --------               --------

Cash flows from investing activities:
Purchase of short-term investments                                                                    (7,676)               (24,231)
Maturities of short-term investments                                                                  14,500                 34,407
Capital expenditures                                                                                    (573)                  (498)
                                                                                                    --------               --------

Net cash provided by investing activities                                                              6,251                  9,678
                                                                                                    --------               --------

Cash flows from financing activities:
Principal payments on notes payable                                                                   (1,065)                  (817)
Net proceeds from issuance of common stock                                                             1,184                    101
                                                                                                    --------               --------

Net cash provided by (used in) financing activities                                                      119                   (716)
                                                                                                    --------               --------

Net (decrease) increase  in cash and cash equivalents                                                 (2,875)                   689
Cash and cash equivalents, beginning of period                                                         5,660                  7,794
                                                                                                    --------               --------
Cash and cash equivalents, end of period                                                            $  2,785               $  8,483
                                                                                                    ========               ========

Supplemental disclosure of cash flow information:
Interest paid                                                                                       $    202               $    270
                                                                                                    ========               ========

                                            See Notes to Condensed Financial Statements.
</TABLE>

                                                                 5

<PAGE>


                         MICROCIDE PHARMACEUTICALS, INC.

                     NOTES TO CONDENSED FINANCIAL STATEMENTS

                               September 30, 2000
                                   (Unaudited)


1.       Summary of Significant Accounting Policies

         Organization and Basis of Presentation

         Microcide Pharmaceuticals,  Inc. (the "Company") is a biopharmaceutical
company  whose  mission  is  to  discover,   develop  and  commercialize   novel
antimicrobials for the improved treatment of serious bacterial, fungal and viral
infections. The Company's discovery and development programs address the growing
problem of bacterial drug  resistance  and the need for improved  antifungal and
antiviral agents through two principal themes: (i) Targeted  Antibiotics,  which
focuses on developing novel antibiotics and antibiotic  potentiators to directly
address existing  bacterial and fungal  resistance  problems,  and (ii) Targeted
Genomics,  which utilizes  bacterial,  fungal and viral genetics to discover new
classes of antimicrobials and other novel treatments for infectious diseases.

         The accompanying  unaudited  condensed  financial  statements have been
prepared in accordance with generally accepted accounting principles for interim
financial  information and with the  instructions to Form 10-Q and Rule 10-01 of
Regulation  S-X.  Accordingly,  they do not include all of the  information  and
footnotes  required by generally  accepted  accounting  principles  for complete
financial statements. In the opinion of management,  all adjustments (consisting
of normal recurring accruals)  considered necessary for a fair presentation have
been included.  The results of operations  for the interim  periods shown herein
are not necessarily indicative of operating results for the entire year.

         This unaudited  financial  data should be read in conjunction  with the
financial  statements and footnotes  contained in the Company's annual report on
Form 10-K for the year ended December 31, 1999.

2.       Net Loss per Share

         Basic  earnings  (loss)  per share is  calculated  using  the  weighted
average  number of common  shares  outstanding.  Because the Company is in a net
loss  position,  diluted  earnings  per share is  calculated  using the weighted
average number of common shares  outstanding and excludes the effects of options
which are antidilutive.  Had the Company been in a net income position,  diluted
earnings  per share would have  included the shares used in the  computation  of
basic net loss per share as well as an additional 1,582,782 and 1,663,176 shares
for 2000 and 1999,  respectively,  related to  outstanding  options not included
above (as determined  using the treasury  stock method at the estimated  average
market value).

3.       Comprehensive Loss

         Comprehensive  loss is  comprised  of net loss and other  comprehensive
income (loss).  Other  comprehensive  income (loss) includes  certain changes in
equity that are excluded from net loss.  Specifically,  unrealized holding gains
and losses on our available-for-sale  securities, which were reported separately
in stockholders'  equity, are included in accumulated other comprehensive income
(loss).

                                       6

<PAGE>


4.       Recently Issued Accounting Standards

         In December 1999, the Securities and Exchange  Commission  issued Staff
Accounting  Bulletin  No. 101 ("SAB  101"),  "Revenue  Recognition  in Financial
Statements."  SAB 101 summarizes  certain areas of the staff's views in applying
generally  accepted  accounting  principles to revenue  recognition.  SAB 101 is
required to be adopted by December  31,  2000.  The Company is in the process of
assessing the impact of SAB 101 and does not expect that the  implementation  of
SAB 101 will have a material effect.

         In March  2000,  the FASB  issued  Interpretation  No.  44 ("FIN  44"),
"Accounting  for  Certain  Transactions  Involving  Stock  Compensation",  which
contains  rules  designed to clarify the  application  of APB 25 with respect to
stock-related  compensation.  FIN 44 is effective  July 1, 2000. The adoption of
FIN 44 did not have a material  impact on the  Company's  financial  position or
results of operations.

5.       Subsequent Events

         In  November  2000,  the  Company  announced  the signing of a research
collaboration  and license  agreement with  Schering-Plough  Animal Health,  for
joint research to discover and develop improved  veterinary  antimicrobial drugs
using  Microcide's  technology and knowledge of bacterial efflux pumps and other
resistance  mechanisms  that  limit  drug  effectiveness.  Under  terms  of  the
agreement,  Schering-Plough Animal Health will have worldwide rights to products
resulting from the  collaboration.  The Company will receive an upfront  payment
and research  support  payments over a two-year period and milestone and royalty
payments on products emerging from the collaboration.

         The Company also recently  announced that Pfizer Animal Health notified
the Company of its decision to extend the Collaborative Research Agreement dated
January 1999 for an additional year, beginning January 2001.


                                       7

<PAGE>


ITEM 2. MANAGEMENT'S  DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
        OF OPERATIONS

Overview

         As  part  of  the  Company's  strategy  to  enhance  its  research  and
development  capabilities  and to  fund,  in  part,  its  capital  requirements,
Microcide entered into collaborative  agreements with four major  pharmaceutical
companies.  Pursuant to the Company's collaborative agreements with R.W. Johnson
Pharmaceutical  Research  Institute,  a Johnson &  Johnson  company  ("RWJPRI"),
Daiichi   Pharmaceutical   Co.   ("Daiichi"),   Pfizer   Inc.   ("Pfizer")   and
Schering-Plough   Animal  Health   Corporation   ("SPAH")  (the   "Collaborative
Agreements"),  the Company has received  license  fees,  milestone  payments and
research  support  payments,  and can potentially  receive  additional  research
support payments,  milestone payments and royalty payments. License payments are
typically  nonrefundable up-front payments for licenses to develop,  manufacture
and  market   products,   if  any,  that  are  developed  as  a  result  of  the
collaboration.  Research support payments are typically  contractually obligated
payments to fund research and  development  over the term of the  collaboration.
Milestone  payments are payments  contingent  upon the  achievement of specified
milestones,   such  as  selection  of  candidates  for  drug  development,   the
commencement of clinical trials or receipt of regulatory approvals. If drugs are
successfully  developed  and  commercialized  as a result  of the  Collaborative
Agreements,  the Company will receive royalty  payments based upon the net sales
of such drugs. In addition,  the Company has derived other revenues  principally
through  the  sale  of   molecular   diversity  to  other   pharmaceutical   and
biotechnology  companies  for  use  in  their  research  programs,  and  through
short-term contract research.

         Through  September 30, 2000,  the Company had received in the aggregate
$52.8 million in license fees,  milestone payments and research support payments
under  the  Collaborative  Agreements.   The  funded  research  portion  of  the
Collaborative  Agreements  with  Daiichi and RWJPRI  concluded at the end of the
first and fourth  quarters  of 1999,  respectively.  In  November  1999,  RWJPRI
commenced  Phase I  clinical  trials  of our  cephalosporin  compound  RWJ 54428
(MC-02,479)  developed  during  the  Microcide-RWJPRI   Gram-positive   research
collaboration.   While   progress   was  made   during   the   quarter   in  the
RWJPRI-sponsored  Phase I clinical trials  involving this compound,  analysis of
data from three  separate  Phase I protocols  indicates the need for  additional
studies to address  local  irritation  at the  injection  site  observed in some
subjects. This decision will extend completion of the current Phase I trials for
this compound  beyond  year-end  2000. In addition,  work  continues on a second
Microcide  cephalosporin  compound,  RWJ  333441  (MC-04,546),  in  pre-clinical
development with RWJPRI.

         In February  2000,  the November 1995 Daiichi  agreement was amended to
focus on advancing a particular  class of efflux pump  inhibitor  compounds  for
pre-clinical development.  The March 1996 Pfizer agreement was amended effective
March 2000, and funding for the fifth year is at a reduced amount.  In May 2000,
the Company and Daiichi  signed a new joint  research  agreement  for a one year
term whereby Daiichi will provide  research support payments for discovering and
developing  inhibitors  that  will  overcome  the  effect  of  efflux  pumps  in
Pseudomonas  aeruginosa.  The Company  also signed an agreement in May 2000 with
Coelacanth  Corporation  for joint  research,  in which  Coelacanth will provide
novel libraries of compounds for screening in a broad range of Microcide  assays
directed  at  the  identification  of  innovative   antiviral,   antifungal  and
antibacterial  therapeutic  agents.  In November 2000, the Company announced the
signing of a research  collaboration  and license agreement with SPAH. The joint
research  effort will use  Microcide's  technology  and  knowledge  of bacterial
efflux  pumps and other  resistance  mechanisms  (see  Subsequent  Events).  The
Company also recently  announced that Pfizer Animal Health  notified the Company
of its decision to extend the  Collaborative  Research  Agreement  dated January
1999 for an additional year, beginning January 2001.

         In the  event  that  the  Company  and its  collaborators  achieve  the
specified research and product  development  milestones,  it will be entitled to
receive milestone payments as follows: up to $16.5 million for the first product
and up to $15.5 million for each additional  product  developed  pursuant to the
RWJPRI  Agreements,  up to $13.0 million for each product developed  pursuant to
the  Daiichi  Agreements  and up to $32.5  million  for each  product  developed
pursuant  to  the  Pfizer   Agreements.   The  Pfizer  Animal  Health  and  SPAH
collaborations  provide  for a lower  level of  milestone  payments  than  those
applicable to human health applications. Receipt of the above milestone payments
is  contingent  upon  achieving   specified  research  and  product  development
milestones,  a number of which may not be achieved for several  years,  if ever.
While the  Collaborative  Agreements  provide  for  royalty  payments  on future
products that may result, the Company does not expect to receive royalties based
upon net sales of drugs for a significant number of years, if at all.

                                       8

<PAGE>


         The Company has incurred  substantial losses in the past and expects to
continue  to incur  operating  losses  over the next  several  years.  Quarterly
results of  operations  are  subject to  significant  fluctuations  based on the
timing and amount of certain revenues earned under the Collaborative Agreements.
Fluctuations  in the  Company's  operating  results  and market  conditions  for
biotechnology  stocks  in  general  could  have  a  significant  impact  on  the
volatility  of the market  price for the common stock and on the future price of
the common stock. The stock market has experienced  significant price and volume
fluctuations that are often unrelated to the operating performance of particular
companies.  The market price of the common stock, like that of the securities of
many other biopharmaceutical companies, has been and is likely to continue to be
highly volatile.

         The biotechnology industry is highly competitive,  and new developments
are  occurring  at  an  increasing  pace.  Competition  from  biotechnology  and
pharmaceutical   companies,   joint   ventures,   academic  and  other  research
institutions and others is intense and is expected to increase. Many competitors
have substantially greater financial, technical and personnel resources than the
Company.  Although the Company  believes that it has identified new and distinct
approaches to drug  discovery,  there are other  companies  with drug  discovery
programs, at least some of the objectives of which are the same as or similar to
the Company's.  Competing  technologies  may be developed which would render the
Company's technologies obsolete or non-competitive.

         This Form 10-Q contains  forward-looking  statements based upon current
expectations,  including  statements  with  regard to the  potential  receipt of
additional research support payments,  milestone payments and royalties from the
Company's    collaborative    partners,    the   successful    development   and
commercialization of drugs and the receipt of royalties thereon or sales revenue
therefrom,  and the period of time for which the  Company's  existing  financial
resources,  interest income and future payments under  Collaborative  Agreements
will be  sufficient  to enable  the  Company to  maintain  current  and  planned
operations,  the continuation of the Company's Collaborative Agreements with its
strategic partners,  the potential impact of any latent Year 2000 issues and the
market  risk  of the  Company's  investments.  Such  forward-looking  statements
involve risks and uncertainties,  including,  without limitation, the following.
There is no assurance that any compounds  discovered will  successfully  proceed
through   pre-clinical   development  and  clinical  trials,   obtain  requisite
regulatory  approvals for marketing or result in a commercially  useful product.
There is no  assurance  that the Company  will  successfully  continue  existing
corporate  collaborations or enter into further  collaborations  with respect to
any of its internally  funded  research  programs or that current  collaborators
will elect to proceed  through the various  stages of  clinical  development  as
currently  anticipated  or on the same  schedule as we would  proceed if we were
conducting such trials independently. There is no assurance that any development
candidates  will be identified,  that any selected  development  candidates will
proceed  through  pre-clinical  trials  or will  prove  safe and  effective  for
treatment of humans or animals in clinical  trials.  There is no assurance  that
the identification,  selection, manufacture,  pre-clinical testing, and clinical
testing of development  candidates will not take substantially  longer or not be
substantially  more  expensive  than  contemplated  by the Company.  There is no
assurance  that the Company will be able to obtain on a timely basis  government
regulatory clearance required for clinical testing, manufacturing, and marketing
of its products. There is no assurance that any latent Year 2000 issues will not
have a material  impact on the  Company.  For a  discussion  of other  risks and
uncertainties  affecting the Company's business, see the Company's annual report
on Form 10-K for the year ended December 31, 1999. The Company's  actual results
and timing of certain events may differ significantly from the results discussed
in such forward-looking statements as a result of these or other factors.

Results of Operations

Three Months Ended September 30, 2000 and September 30, 1999

Revenues.  Total  revenues for the third quarter of 2000 were $1.5  million,  as
compared to $1.6  million in the third  quarter of 1999.  Revenues  were largely
derived from the corporate  collaborations with Pfizer, Pfizer Animal Health and
Daiichi.  The decline in comparative  revenues from RWJPRI and Pfizer was offset
by an increase in research  support  revenues from the joint research  agreement
signed in May 2000 with  Daiichi  and  contract  research  revenues  from  other
companies funding exploratory research.

                                       9

<PAGE>


Research and Development  Expenses.  Research and  development  expenses for the
third  quarters  were  approximately  the  same in both  2000  and  1999 at $4.0
million.

General and Administrative Expenses. General and administrative expenses for the
third  quarter  increased  slightly from $1.1 million in 1999 to $1.2 million in
2000, due primarily to higher expense for outside services.

Interest  Income,  net.  Interest  income for the third quarter  decreased  from
$343,000  in 1999 to $268,000  in 2000,  primarily  due to a decrease in average
cash  balances.  Interest  expense for the third quarter of 2000  decreased from
$82,000 in 1999 to $59,000 in 2000 primarily due to the declining  balance on an
equipment financing loan.

Nine Months Ended September 30, 2000 and September 30, 1999

Revenues.  Total revenues for the first nine months of 2000 were $4.1 million, a
decrease  from $5.8 million in revenues  recognized  in the first nine months of
1999.  Revenues  were largely  derived from the  corporate  collaborations  with
Pfizer,  Pfizer  Animal  Health and Daiichi.  The decrease in revenues  resulted
primarily  from a reduction in funding  from Pfizer due to a contract  amendment
that  modified the research  plan,  and the  conclusion  of the funded  research
portion of the  collaboration  with RWJPRI in December  1999.  The  decrease was
partially  offset  by  research  revenues  recognized  from the  joint  research
agreement signed with Daiichi in May 2000, and contract  research  revenues from
other companies funding exploratory research.

Research and Development  Expenses.  Research and  development  expenses for the
first nine months of 2000  decreased from $13.2 million in 1999 to $12.2 million
in 2000. The decrease was due primarily to lower compensation expenses resulting
from a decrease  in  headcount  and lower  spending  for  outside  services  and
research supplies.

General and Administrative Expenses. General and administrative expenses for the
first nine months of 2000 increased from $3.1 million in 1999 to $3.2 million in
2000. The increase was due primarily to higher expense for outside services.

Interest  Income,  net.  Interest  income  for the  first  nine  months  of 2000
decreased  from $1.1  million in 1999 to  $878,000 in 2000,  primarily  due to a
decrease in average cash balances. Interest expense for the first nine months of
2000  decreased  from $270,000 in 1999 to $202,000 in 2000  primarily due to the
declining balance on an equipment financing loan.

Liquidity and Capital Resources

         The Company has  financed  its  operations  since  inception  primarily
through  the  sale of  equity  securities,  through  funds  provided  under  the
Collaborative Agreements, through other revenues principally consisting of sales
of molecular diversity and contract research and through equipment financing. As
of September 30, 2000,  the Company had received  $66.0 million from the sale of
equity and $52.8  million in cash from license and  milestone  fees and research
support payments under the Collaborative Agreements.

         Cash, cash equivalents and short-term investments at September 30, 2000
were $15.2 million  compared to $24.9 million at December 31, 1999. The decrease
during  the  first  nine  months  of 2000  was  due  primarily  to cash  used by
operations of $9.3 million,  $573,000 in capital  expenditures  and $1.1 million
utilized in financing  activities,  mainly  principal  payments on the Company's
equipment  financing  arrangement.  This decrease was  partially  offset by $1.2
million in net  proceeds  from the issuance of common stock from the exercise of
stock options.

         The Company  expects  that its  existing  capital  resources,  interest
income and future  payments due under the  Collaborative  Agreements will enable
the Company to maintain  current and planned  operations  at least through 2001.
The Company expects that it will need to seek  additional  funds to continue its
business  activities and will seek to raise such  additional  funding from other
collaborative arrangements, or public or private financings,  including sales of
equity or debt  securities.  Any such  collaborative  or licensing  arrangements
could  result  in   limitations   on  the  Company's   ability  to  control  the
commercialization  of resulting drugs, if any, and could limit profits,  if any,
therefrom.  Any such equity  financing could result in dilution to the Company's
then-existing stockholders. There can be no assurance that additional funds will
be available on favorable terms or at all, or that such funds, if raised,  would
be  sufficient to permit the

                                       10

<PAGE>


Company to  continue  to  conduct  its  operations.  If  adequate  funds are not
available, the Company may be required to curtail significantly or eliminate one
or more of its research programs.

Impact of Year 2000

         In prior  periods,  the  Company  has  discussed  its plans and  status
relating to potential computer system  malfunctions  relating to the "Year 2000"
issue,  whereby computer systems would not be able to distinguish  between dates
in the 20th century versus the 21st century. In late 1999, the Company completed
its  assessment,  repair,  upgrade and  replacement of its computer  systems and
research  equipment,  as well as an analysis of the  readiness of third  parties
with whom the Company  interacts.  As a result of its planning  and  remediation
efforts,  the Company experienced no significant  disruptions in its information
technology  and  non-information  technology  systems  and  believes  that those
systems successfully responded to the Year 2000 date change.

         As of  September  30,  2000,  the Company is not aware of any  material
problems  resulting from Year 2000 issues,  either with its computer  systems or
research equipment with embedded chips or software. The Company will continue to
monitor  its  information  technology  systems  and those of its  suppliers  and
vendors  throughout  the Year 2000 to ensure that any latent  Year 2000  matters
that may arise are  addressed  promptly.  Management  does not believe  that any
latent Year 2000 changes will have a material  adverse  impact on the  Company's
financial condition or results of operations. To date, costs related to the Year
2000 issues have not been material.

                                       11

<PAGE>


ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

         The following  discussion  about the Company's  market risk  disclosure
involves  forward-looking  statements.  The  Company is  exposed to market  risk
related  mainly to changes in interest  rates.  The  Company  does not invest in
derivative financial instruments.

Interest Rate Sensitivity

         The fair value of the Company's investments in marketable securities at
September  30, 2000 was $13.9  million.  The Company's  investment  policy is to
manage its marketable  securities  portfolio to preserve principal and liquidity
while  maximizing  the  return  on  the  investment  portfolio.   The  Company's
marketable   securities  portfolio  is  primarily  invested  in  corporate  debt
securities with an average  maturity of under one year and a minimum  investment
grade rating of A or A-1 or better to minimize credit risk.  Although changes in
interest rates may affect the fair value of the marketable  securities portfolio
and cause unrealized gains or losses, such gains or losses would not be realized
unless the investments are sold prior to maturity.

Foreign Currency Exchange Risk

         At this time, the Company does not participate in any foreign  currency
exchange activities, and therefore is not subject to risk of gains or losses for
changes in foreign exchange rates.

                                       12

<PAGE>


PART II      OTHER INFORMATION

Item 1.      Legal Proceedings

             None.

Item 2.      Changes in Securities

             None.

Item 3.      Defaults in Senior Securities

             None.

Item 4.      Submission of Matters to a Vote of Security Holders

             None.

Item 5.      Other Information

             None.

Item 6.      Exhibits and Reports on Form 8-K

     (a)     The following exhibits have been filed with this report:

             10.32*  Research  Collaboration  and License  Agreement between the
                     Registrant and  Schering-Plough  Animal Health  Corporation
                     and Schering-Plough Ltd. effective September 1, 2000.

             27.1    Financial Data Schedule

     (b)     Reports on Form 8-K.

             No  reports  on Form  8-K  were  filed  during  the  quarter  ended
             September 30, 2000.

             * To be filed by amendment.



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<PAGE>


                                   SIGNATURES


         Pursuant to the  requirements  of the Securities  Exchange Act of 1934,
the  registrant  has duly  caused  this report to be signed on its behalf by the
undersigned, thereunto duly authorized.


Dated:   November 14, 2000


                                           MICROCIDE PHARMACEUTICALS, INC.
                                           (Registrant)



                                            /s/  James E. Rurka
                                           -------------------------------------
                                           James E. Rurka
                                           President, Chief Executive Officer
                                           and Director, (principal executive
                                           officer)


                                            /s/  Donald D. Huffman
                                           -------------------------------------
                                           Donald D. Huffman
                                           Vice President, Finance and Corporate
                                           Development, Chief Financial Officer
                                           (principal financial and accounting
                                           officer)

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